We consider a class of nonlinear integro-differential equations that model degenerate nonlocal diffusion. We investigate whether the strong maximum principle is valid for this nonlocal equation. For degenerate parabolic PDEs, the strong maximum principle is not valid. In contrast, for nonlocal diffusion, we can formulate a strong maximum principle for nonlinearities satisfying a geometric condition related to the flux operator of the equation. In our formulation of the strong maximum principle, we find a physical re-interpretation and generalization of the standard PDE conclusion of the principle: we replace constant solutions with solutions of zero flux. We also consider nonlinearities outside the scope of our principle. For highly degenerate conductivities, we demonstrate the invalidity of the strong maximum principle. We also consider intermediate, inconclusive examples, and provide numerical evidence that the strong maximum principle is valid. This suggests that our geometric condition is sharp.